For the purpose of ensuring chemical propriety, the carved out surface needs to be processed based on a set of rules as proposed by Coasne et al. (2008).
First, all unsaturated silicon atoms are to be removed. Next, silicon atoms with three unsaturated oxygen bonds are eliminated. Finally, now unbound oxygen atoms must be deleted. The resulting surface has fully saturated silicon atoms with a maximum of two unsaturated oxygen bonds.
These unsaturated oxygens will be used as binding sites to connect molecules that are to be placed on the surface.